<div dir="ltr">Dear <span style="font-size:12.8px">Huawang,</span><div><span style="font-size:12.8px"><br></span></div><div><div><span style="font-size:12.8px">The tool will automatically recognize most of the labels from Phenix and CCP4 </span></div><div><span style="font-size:12.8px">and convert them to appropriate labels for mmCIF format. If some labels are not recognized,</span></div><div><span style="font-size:12.8px">or another mmCIF labels are needed for them, one may use mtz_labels and </span></div><div><span style="font-size:12.8px">cif_labels parameters to provide pairs of mtz and cif labels. Note that provided</span></div><div><span style="font-size:12.8px">cif_labels must comply with mmCIF format. Number of mtz_labels should be equal</span></div><div><span style="font-size:12.8px">to number of cif_labels.</span></div></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">In command-line, for example:</span></div><div><div style=""><span style="font-size:12.8px">phenix.mtz_as_cif data.mtz output_file=custom.cif mtz_labels="FOBS SIGFOBS" </span></div><div style=""><span style="font-size:12.8px"> cif_labels="_refln.custom1 _refln.custom2"</span></div></div><div style=""><span style="font-size:12.8px">Or you can put these instructions in .eff file.</span></div><div style=""><span style="font-size:12.8px">Basically, mtz_labels and cif_labels are just white-space separated lists. In this example FOBS will become _refln.custom1 and SIGFOBS will become _refln.custom2.</span></div><div style=""><span style="font-size:12.8px"><br></span></div><div style=""><span style="font-size:12.8px">To find out what labels you have in mtz file you may use phenix.mtz.dump utility.</span></div><div style=""><span style="font-size:12.8px"><br></span></div><div style=""><span style="font-size:12.8px">Also note, that this functionality is available in GUI: Utilities-> Convert MTZ to mmCIF.</span></div><div style=""><span style="font-size:12.8px"><br></span></div><div style=""><span style="font-size:12.8px">Hope this helps,</span></div><div style=""><span style="font-size:12.8px">Best regards,</span></div><div style=""><span style="font-size:12.8px">Oleg Sobolev.</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Aug 25, 2016 at 11:58 AM, Huanwang Yang <span dir="ltr"><<a href="mailto:hyang@rcsb.rutgers.edu" target="_blank">hyang@rcsb.rutgers.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Dear Oleg,<br>
<br>
Thank you so much for your help.<br>
In the parameter file, what should I give to the labels below<span class=""><br>
<br>
<div><span style="font-size:12.8px"> mtz_labels = None</span></div>
<div><span style="font-size:12.8px"> cif_labels = None</span></div>
<br></span>
Could you provide an simple example for them? Thanks a lot.<br>
<br>
Best,<br>
Huawang<span class=""><br>
<br>
<br>
On 08/25/2016 01:49 PM, Oleg Sobolev wrote:<br>
</span></div><span class="">
<blockquote type="cite">
<div dir="ltr">
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">Please find some about
phenix.mtz_as_cif usage below. In the next nightly build it
will be displayed if you run the tool without arguments.
Please let me know if you need additional information.</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">Best regards,</span></div>
<div><span style="font-size:12.8px">Oleg Sobolev.</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div>
<div><span style="font-size:12.8px">phenix.mtz_as_cif:
Convert mtz to CIF format.</span></div>
<div><span style="font-size:12.8px">Usage:
phenix.mtz_as_cif data.mtz [params.eff] [options ...]</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">Usage examples:</span></div>
<div><span style="font-size:12.8px">
phenix.mtz_as_cif data.mtz</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">------------------------------<wbr>------------------------------<wbr>-------------------</span></div>
<div><span style="font-size:12.8px">mtz_as_cif {</span></div>
<div><span style="font-size:12.8px"> mtz_file = None</span></div>
<div><span style="font-size:12.8px"> output_file =
None</span></div>
<div><span style="font-size:12.8px"> mtz_labels =
None</span></div>
<div><span style="font-size:12.8px"> cif_labels =
None</span></div>
<div><span style="font-size:12.8px">}</span></div>
</div>
</div>
<div class="gmail_extra"><br>
</div>
</blockquote>
<br>
</span></div>
</blockquote></div><br></div>